SAXSdb — 5ce3

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1. Protein Identity and Related Structures Protein Identity & Related Structures

Actin

OrganismNot specified

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 2	Protein kinase YopO × 1 （Q93KQ6） ADENOSINE-5'-TRIPHOSPHATE × 1 CALCIUM ION × 1 ADENOSINE-5'-DIPHOSPHATE × 1 MAGNESIUM ION × 1 water × 2	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 2	Protein kinase YopO × 1 （Q93KQ6） ADENOSINE-5'-TRIPHOSPHATE × 1 CALCIUM ION × 1 ADENOSINE-5'-DIPHOSPHATE × 1 MAGNESIUM ION × 1 water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	G3CKA6_SPOFR
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–376； UniProt 1–376 Author chain C； PDBConstruct 1–376； UniProt 1–376

Protein kinase YopO

Yersinia enterocolitica

UniProt Q93KQ6

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 2	Actin × 1 （G3CKA6） ADENOSINE-5'-TRIPHOSPHATE × 1 CALCIUM ION × 1 ADENOSINE-5'-DIPHOSPHATE × 1 MAGNESIUM ION × 1 water × 2	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 2	Actin × 1 （G3CKA6） ADENOSINE-5'-TRIPHOSPHATE × 1 CALCIUM ION × 1 ADENOSINE-5'-DIPHOSPHATE × 1 MAGNESIUM ION × 1 water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	Q93KQ6_YEREN
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain B； PDBConstruct 3–643； UniProt 89–729 Author chain D； PDBConstruct 3–643； UniProt 89–729

The page prioritizes protein identity, the current assembly, associated components, oligomeric state and cross-PDB links. Chain mapping and sequence ranges are retained as data evidence. Internal IDs, import timestamps and assembly operation expressions are maintenance fields and are not shown here.

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2. Structure Basics 2. Structure Basics

Entry ID entry_id	5ce3
Deposition date deposition_date	2015-07-06
Structure title title	The Yersinia YopO - actin complex with MgADP
Keywords keywords	Kinase cytoskeleton Pathogen host, CONTRACTILE PROTEIN-TRANSFERASE complex; CONTRACTILE PROTEIN/TRANSFERASE
Experimental Method method	X-RAY DIFFRACTION

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3. Official assembly/model SAXS Official SAXS Profiles

This page reads only the latest assembly calculations. Every curve maps to an explicit PDB entry, official biological assembly and coordinate model.

5ce3__assembly_1__model_1

Assembly 1 · Model 1 · CRYSOL 4.1.3-1-20251215 (887e7ef)

Download this curve (.dat)

5ce3__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

5ce3__assembly_1__model_1 | P(r) · Pending

P(r) will be calculated and displayed separately for the same assembly/model.

Rg（Guinier）	34.49 Å
Rg (electron density)	34.09 Å
Total Rg	34.54 Å
Atom count	7556
Residues	956
Excluded volume	134130 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`5ce3__assembly_1__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`5ce3__assembly_2__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download

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4. Crystallography and Experiment 4. Crystallography & Experiment

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5. Entities and Polymers Entities & Polymers (7)

Entity 1 Entity 1 polymer

Description description	Actin
Molecular weight formula_weight	41755.6 kDa
Source method src_method	nat
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,C
Atom count atom_count	15121

MCDDDVAALVVDNGSGMCKAGFAGDDAPRAVFPSIVGRPRHQGVMVGMGQKDSYVGDEAQSKRGILTLKYPIEHGIITNWDDMEKIWHHTFYNELRVAPEEHPVLLTEAPLNPKANREKMTQIMFETFNSPAMHVAIQAVLSLYASGRTTGIVLDSGDGVSHTVPIYEGYALPHAILRLDLAGRDLTDYLMKILTERGYSFTTTAEREIVRDIKEKLCYVALDFEQEMATAAASTSLEKSYELPDGQVIAIGNERFRCPEALFQPSFLGMESCGIHETVYNSIMKCDVDIRKDLYANTVMSGGTTMYPGIADRMQKEITALAPSTIKTKIIAPPERKYSVWIGGSILASLSTFQQMWISKEEYDESGPGIVHRKCF

Entity 2 Entity 2 polymer

Description description	Protein kinase YopO
Molecular weight formula_weight	71776.9 kDa
Mutation mutation	K205Y, E206Y, E207Y, K440Y, K441Y
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B,D

GPTSQELRSDIPNALSNLFGAKPQTELPLGWKGKPLSGAPDLEGMRVAETDKFAEGESHISIIETKDKQRLVAKIERSIAEGHLFAELEAYKHIYKTAGKHPNLANVHGMAVVPYGNRYYYALLMDEVDGWRCSDTLRSLADSWKQGKINSEAYWGTIKFIAHRLLDVTNHLAKAGIVHNDIKPGNVVFDRASGEPVVIDLGLHSRSGEQPKGFTESFKAPELGVGNLGASEKSDVFLVVSTLLHGIEGFEKDPEIKPNQGLRFITSEPAHVMDENGYPIHRPGIAGVETAYTRFITDILGVSADSRPDSNEARLHEFLSDGTIDEESAKQILKDTLTGEMSPLPTDVRRITPYYLRELSDLLRTHLSSAATKQLDMGVVLSDLDTMLVALDKAEREGGVDKDQLKSFNSLILKTYSVIGAYIKGREGDTKSSSTEVSPYHRSNFMLSIVEPSLQRIQKHLDQTHSFSDIGSLMRAHKHLETLLEVLVTLSQQGQPVSSETYSFLNRLAEAKVTLSQQLNTLQQQQESAKAQLSILINRSGSWADVARQSLQRFDSTRPVVKFGTEQYTAIHRQMMAAHAAITLQEVSEFTDDMRNFTADSIPLLIQLGRSSLMDEHLVEQREKLRELTTIAERLNRLEREWM

Source Source

Source organism organism	Yersinia enterocolitica
NCBI taxonomy ID ncbi_taxonomy_id	630
Host organism host_organism	Escherichia coli

Entity 3 Entity 3 non-polymer

Description description	ADENOSINE-5'-TRIPHOSPHATE
Molecular weight formula_weight	507.2 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 4 Entity 4 non-polymer

Description description	CALCIUM ION
Molecular weight formula_weight	40.1 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 5 Entity 5 non-polymer

Description description	ADENOSINE-5'-DIPHOSPHATE
Molecular weight formula_weight	427.2 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 6 Entity 6 non-polymer

Description description	MAGNESIUM ION
Molecular weight formula_weight	24.3 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 7 Entity 7 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	9

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6. Fold Classification (SCOP + CATH) 10 domains

SCOP 2.08 (4 domains)

Domain ID domain_id	d5ce3a1
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.55 — Ribonuclease H-like motif
Superfamily Superfamily superfamily	c.55.1 — Actin-like ATPase domain
Family Family family	c.55.1.0 — automated matches

Domain ID domain_id	d5ce3a2
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.55 — Ribonuclease H-like motif
Superfamily Superfamily superfamily	c.55.1 — Actin-like ATPase domain
Family Family family	c.55.1.1 — Actin/HSP70

Domain ID domain_id	d5ce3c1
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.55 — Ribonuclease H-like motif
Superfamily Superfamily superfamily	c.55.1 — Actin-like ATPase domain
Family Family family	c.55.1.0 — automated matches

Domain ID domain_id	d5ce3c2
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.55 — Ribonuclease H-like motif
Superfamily Superfamily superfamily	c.55.1 — Actin-like ATPase domain
Family Family family	c.55.1.1 — Actin/HSP70

CATH v4.4 (6 domains)

Domain ID domain_id	5ce3A01
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	420 — Nucleotidyltransferase; domain 5
Homologous superfamily homologous superfamily	40 — ATPase, nucleotide binding domain

Domain ID domain_id	5ce3A02
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	420 — Nucleotidyltransferase; domain 5
Homologous superfamily homologous superfamily	40 — ATPase, nucleotide binding domain

Domain ID domain_id	5ce3A03
Class class	3 — Alpha Beta
Architecture architecture	90 — Alpha-Beta Complex
Topology topology	640 — Actin; Chain A, domain 4
Homologous superfamily homologous superfamily	10 — ATPase, substrate binding domain, subdomain 4

Domain ID domain_id	5ce3C01
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	420 — Nucleotidyltransferase; domain 5
Homologous superfamily homologous superfamily	40 — ATPase, nucleotide binding domain

Domain ID domain_id	5ce3C02
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	420 — Nucleotidyltransferase; domain 5
Homologous superfamily homologous superfamily	40 — ATPase, nucleotide binding domain

Domain ID domain_id	5ce3C03
Class class	3 — Alpha Beta
Architecture architecture	90 — Alpha-Beta Complex
Topology topology	640 — Actin; Chain A, domain 4
Homologous superfamily homologous superfamily	10 — ATPase, substrate binding domain, subdomain 4

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Unit-cell length a length_a	108.730 Å
Unit-cell length b length_b	121.750 Å
Unit-cell length c length_c	118.580 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	104.88 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	4

Space group space_group	P 1 21 1
Space-group number int_tables_number	4
Crystal system crystal_system	—

Resolution resolution	2.930 Å
Low-resolution limit resolution_low	114.600 Å
R factor r_factor	0.1981
R_work r_work	0.1959
R_free r_free	0.2402

The Yersinia YopO - actin complex with MgADP

1. Protein Identity and Related Structures Protein Identity & Related Structures

Actin

State in the Current Structure

Other States of the Same Protein in the Database

Protein kinase YopO

State in the Current Structure

Other States of the Same Protein in the Database

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

5ce3__assembly_1__model_1

5ce3__assembly_1__model_1 | I(q)

5ce3__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

5. Entities and Polymers Entities & Polymers (7)

Entity 1 Entity 1 polymer

Polymer Polymer

Entity 2 Entity 2 polymer

Polymer Polymer

Source Source

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 non-polymer

Entity 7 Entity 7 water

6. Fold Classification (SCOP + CATH) 10 domains

SCOP 2.08 (4 domains)

CATH v4.4 (6 domains)

7. Citations (1)

The Yersinia YopO - actin complex with MgADP

1. Protein Identity and Related Structures Protein Identity & Related Structures

Actin

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Protein kinase YopO

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

5ce3__assembly_1__model_1

5ce3__assembly_1__model_1 | I(q)

5ce3__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

5. Entities and Polymers Entities & Polymers (7)

Entity 1 Entity 1 polymer

Polymer Polymer

Entity 2 Entity 2 polymer

Polymer Polymer

Source Source

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 non-polymer

Entity 7 Entity 7 water

6. Fold Classification (SCOP + CATH) 10 domains

SCOP 2.08 (4 domains)

CATH v4.4 (6 domains)

7. Citations (1)